John Scott is an FBI Agent. At the time of his death, he was working undercover with the NSA in order to infiltrate a bio-terrorism cell run by weapons dealer Conrad Moreau. He was also romantically involved with his law enforcement partner, Agent Olivia Dunham.

Agent Scott (Pilot) was summoned to investigate Flight 627. Following up leads back at FBI headquarters, Scott and Olivia were sent to U-Case Storage to investigate some suspicious activity. Agent Scott discovered a secret laboratory in one of the storage rooms, and its owner Richard Steig. After a chase through the storage facility, Steig detonated some explosives, injuring Scott and knocking Olivia unconscious. The explosion also exposed Scott to synthetic chemicals that were in the labs, afflicting him with the same symptoms as the Flight 627 passengers; albeit with a much slower rate of tissue decay.

Scott was taken to a medical facility and monitored in the Kennedy Wing Isolation Unit, where he was put into a drug induced coma in an attempt to slow down his dissolving tissue.

Olivia searched for a cure, involving Peter and Walter Bishop along the way, and set up a Synaptic Transfer to talk to Scott. Scott is able to share his memories with her and shows her Steig's face. After Olivia identifies Steig and tracks him down in South Boston, Steig co-operates and provides them with a full inventory of the chemicals Scott was exposed to, allowing Walter Bishop to synthesize a cure.

Once cured, Scott recovers almost as rapidly as he degenerated. At this point Olivia discovers that Scott had threatened Steig and knew about the Flight 627 contagion already, but before she can confront him, Scott gains entry to Steig's room in the hospital and suffocates him with a pillow. He then leaves the hospital and drives away but is spotted by Olivia, who gives chase. When he sees Olivia following him he panics and attempts to drive her off the road, but he drives up a maintenance ramp, flipping his car and suffering fatal injuries to his head. He crawls from the car and, in his last moments, tells Olivia to question why Broyles sent them to the U-Case Storage facility. After this he succumbs to his head injuries and dies.

In The Ghost Network, Scott is given a hero's funeral: formal and closed-casket. But later, Massive Dynamic still has John's corpse and is attempting to harvest information and data from a glass disc recovered from Scott's hand. Scott's body remains intact, and in their care.

In The Arrival, Olivia Dunham receives a phone call, and as a man's voice says "Hello Olivia", she reluctantly asks "John?". The connection is broken, and when she calls the Bureau attempting to trace the call, she is informed that there hasn't been any call at all. A printed obituary seen in this episode indicates that Scott was 42 years old at the time of his death.

A couple of days later as she enters her home, she is approached by someone looking exactly like Scott. Dunham later describes the incident to Charlie Francis, adding that when she reached for her weapon, the figure disappeared.

In Power Hungry, Scott speaks to Dunham twice. On the first occasion, after Dunham accuses him of trying to kill her, he responds that it was not him. On the second occasion, he kisses her. While they are kissing, Peter walks up behinds Olivia but can not see John. Walter explains that it's possible that a portion of Agent Scott's consciousness remained with Olivia as a result of the synaptic transfer conducted in Pilot. Scott later leads Dunham to a basement filled with files of investigations he was conducting on his own of Pattern-related incidents.

In The Dreamscape, Olivia sees Scott at the scene of Mark Young's death. She later receives an e-mail from him containing a basement address, which leads to a major break in the case. However, Olivia has been frustrated with these appearances by Scott and demands to Walter that she be put back in the sensory deprivation tank to rid her consciousness of Scott's. Once inside, she witnesses their first date, and John seems to notice Olivia, even though Walter said such a thing is impossible. Olivia uses John's memories to find a suspect, George Morales. Later on, George Morales hallucinates John Scott slitting his throat, which manifests as a real event, killing him. At the end of the episode, Olivia receives another email from John, reading "I SAW YOU. IN THE RESTAURANT."

In Safe, Nina Sharp learns the effort to retrieve Scott's memories has hit a dead end. Scott's body is still in an oxygen chamber and Nina is seriously concerned to learn what else he knows. She later discovers that he shared consciousness with Olivia shortly before his death, bringing Nina to the conclusion that the memories they need may be in Dunham's mind.

In The Transformation, Olivia returns to the sensory deprivation tank to talk with John in order to gain critical information about a case. John shares that he, along with Marshall Bowman and Daniel Hicks, were all working undercover for the NSA, in order to infiltrate the bio-terrorist cell run by Conrad Moreau.

In Brown Betty, his picture is held by fictional Olivia while Walter tells a tale of the man who broke her heart.